It's pretty likely that your color index is the problem. I can;t say I know for sure without checking it over myself, but these results are typical of a map that has been made without first setting the image's properties to indexed color, and selecting a specific indexed palette to work from.
Color index basically means that the image will use one of 256 specific colors, which are specified in the index you chose for the image. These arent preset and will differ from one index to another depending on its purpose. When the mapping program looks at your image to decide what terrain it should place, it isnt checking the color itself... its checking whether the area of the bmp is color #1, 2, 102, all the way to 256, in the index. If you havent set the image up right to use indexed colors, the program will be confused as to which terrain is represented by which color, and may make some incorrect guesses.
If you think this may be your problem or want more help, MSN me at
swordjester2004@hotmail.com . If youre using Photoshop I can probably tell you offhand how to fix it, otherwise we can at least try to figure out what else the problem could be.